phasing.py 文件源码

def extend(self, extensions: List[Tuple[Node]],
               ext_read_sets: List[Set[OrientedRead]]) -> 'HaplotypeSet':
        """Extend the haplotype set with a new set of paths."""

        # Make a copy of itself for a new set
        new_set = HaplotypeSet(self.ploidy, copy_from=self)

        for hap_num, (extension, read_set) in enumerate(
                zip(extensions, ext_read_sets)):
            haplotype_nodes = new_set.haplotypes[hap_num]

            # Add the nodes of the extension to each haplotype
            # It's possible that the last node of this haplotype set
            # (which is probably a bubble exit), is also the bubble entrance
            # and thus our start node of our extension.
            if (len(haplotype_nodes) > 0 and
                    haplotype_nodes[-1] == extension[0]):
                haplotype_nodes.extend(extension[1:])
            else:
                haplotype_nodes.extend(extension)

            new_set.read_sets[hap_num].update(read_set)

        return new_set